Color

One can color the atoms using the following scheme:

  • Element

  • Random

  • Uniform

  • Index

  • Attribute

Color by element

Supported style are:

  1. JMOL: http://jmol.sourceforge.net/jscolors/#color_U

  2. VESTA: https://jp-minerals.org/vesta/en/

  3. CPK: https://en.wikipedia.org/wiki/CPK_coloring

Custom color for each species

Use can set custom color for each species. The color can be in the form of hex code or color name.

[1]:

from ase.build import molecule
from weas_widget import WeasWidget

atoms = molecule("C2H6SO")
viewer = WeasWidget()
viewer.from_ase(atoms)
# set the color and radius for each species
viewer.avr.species.settings["C"].update({"color": "red", "radius": 1.0})
viewer.avr.species.settings["H"].update({"color": "green", "radius": 0.5})
viewer.avr.species.settings["O"].update({"color": "blue", "radius": 0.6})
viewer.avr.species.settings["S"].update({"color": "yellow", "radius": 1.2})
viewer

[1]:

Color by attribute

Coloring based on the attribute of the atoms. The attribute can be: charge, magmom, or any other attribute in the structure.

Here we show how to color the atoms by their forces.

[2]:

from ase.build import bulk
from ase.calculators.emt import EMT
import numpy as np
from weas_widget import WeasWidget
atoms = bulk('Au', cubic = True)
atoms *= [3, 3, 3]
atoms.positions += np.random.random((len(atoms), 3))
atoms.calc = EMT()
atoms.get_potential_energy()
# set the forces as an attribute
atoms.set_array("Force", atoms.calc.results["forces"])
viewer = WeasWidget()
viewer.from_ase(atoms)
viewer.avr.color_by = "Force"
viewer.avr.color_ramp = ["red", "yellow", "blue"]
viewer.avr.model_style = 1
viewer

[2]: